1
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Dong J, Zeng Z, Huang Y, Chen C, Cheng Z, Zhu Q. Challenges and opportunities for circRNA identification and delivery. Crit Rev Biochem Mol Biol 2023; 58:19-35. [PMID: 36916323 DOI: 10.1080/10409238.2023.2185764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Circular RNAs (circRNAs) are evolutionarily conserved noncoding RNAs with tissue-specific expression patterns, and exert unique cellular functions that have the potential to become biomarkers in therapeutic applications. Therefore, accurate and sensitive detection of circRNA with facile platforms is essential for better understanding of circRNA biological processes and circRNA-related disease diagnosis and prognosis; and precise regulation of circRNA through efficient delivery of circRNA or siRNA is critical for therapeutic purposes. Here, we reviewed the current development of circRNA identification methodologies, including overviewing the purification steps, summarizing the sequencing methods of circRNA, as well as comparing the advantages and disadvantages of traditional and new detection methods. Then, we discussed the delivery and manipulation strategies for circRNAs in both research and clinic treatment. Finally, the challenges and opportunities of analyzing circRNAs were addressed.
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Affiliation(s)
- Jiani Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Zhuoer Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China.,Division of Biomedical Engineering, The James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Ying Huang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
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2
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Sun H, Yang Y, Ma Y, Li N, Tan J, Sun C, Li H. Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli. Front Vet Sci 2022; 9:1005899. [PMID: 36187840 PMCID: PMC9521048 DOI: 10.3389/fvets.2022.1005899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Avian pathogenic E. coli (APEC), one of the widespread zoonotic-pathogen, can cause a series of diseases collectively known as colibacillosis. This disease can cause thousands of million dollars economic loss each year in poultry industry and threaten to human health via meat or egg contamination. However, the detailed molecular mechanism underlying APEC infection is still not fully understood. Circular RNAs, a new type of endogenous noncoding RNA, have been demonstrated to involve in various biological processes. However, it is still not clear whether the circRNAs participate in host response against APEC infection. Herein, we utilized the high-throughput sequence technology to identify the circRNA expression profiles in APEC infected HD11 cells. A total of 49 differentially expressed (DE) circRNAs were detected in the comparison of APEC infected HD11 cells vs. wild type HD11 cells, which were involved in MAPK signaling pathway, Endocytosis, Focal adhesion, mTOR signaling pathway, and VEGF signaling pathway. Specifically, the source genes (BRAF, PPP3CB, BCL2L13, RAB11A, and TSC2) and their corresponding DE circRNAs may play a significant role in APEC infection. Moreover, based on ceRNA regulation, we constructed the circRNA-miRNA network and identified a couple of important regulatory relationship pairs related to APEC infection, including circRAB11A-gga-miR-125b-3p, circRAB11A-gga-miR-1696, and circTSC2-gga-miR-1649-5p. Results indicate that the aforementioned specific circRNAs and circRNA-miRNA network might have important role in regulating host immune response against APEC infection. This study is the first time to investigate the circRNAs expression profile and the biological function of the source genes of the identified DE circRNAs after APEC infection of chicken HD11 cells. These results would contribute to a better understanding of the molecular mechanisms in host response against APEC infection.
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Affiliation(s)
- Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Hongyan Sun
| | - Yexin Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Nayin Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jishuang Tan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Changhua Sun
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
- Huan Li
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3
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Liu H, Nwafor CC, Piao Y, Li X, Zhan Z, Piao Z. Identification and Characterization of Circular RNAs in Brassica rapa in Response to Plasmodiophora brassicae. Int J Mol Sci 2022; 23:5369. [PMID: 35628175 PMCID: PMC9141718 DOI: 10.3390/ijms23105369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Plasmodiophora brassicae is a soil-borne pathogen that attacks the roots of cruciferous plants and causes clubroot disease. CircRNAs are noncoding RNAs, widely existing in plant and animal species. Although knowledge of circRNAs has been updated continuously and rapidly, information about circRNAs in the regulation of clubroot disease resistance is extremely limited in Brassica rapa. Here, Chinese cabbage (BJN 222) containing clubroot resistance genes (CRa) against P. brassicae Pb4 was susceptible to PbE. To investigate the mechanism of cicRNAs responsible for clubroot disease resistance in B. rapa, circRNA-seq was performed with roots of 'BJN 222' at 0, 8, and 23 days post-inoculated (dpi) with Pb4 and PbE. A total of 231 differentially expressed circRNAs were identified between the groups. Based on the differentially expressed circRNAs, the circRNA-miRNA-mRNA network was constructed using the target genes directly or indirectly related to plant resistance. Upregulated novel_circ_000495 suppressed the expression of miR5656-y, leading to the upregulation of Bra026508, which might cause plant resistance. Our results provide new insights into clubroot resistance mechanisms and lay a foundation for further studies exploring complex gene regulation networks in B. rapa.
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Affiliation(s)
- Huishan Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Chinedu Charles Nwafor
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Yinglan Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
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4
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Liu D, Fang L. Current research on circular RNAs and their potential clinical implications in breast cancer. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0275. [PMID: 34018386 PMCID: PMC8330541 DOI: 10.20892/j.issn.2095-3941.2020.0275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is one of the most common cancers and the leading causes of death among women worldwide, and its morbidity rate is growing. Discovery of novel biomarkers is necessary for early BC detection, treatment, and prognostication. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs with covalently closed continuous loops, have been found to have a crucial role in tumorigenesis. Studies have demonstrated that circRNAs are aberrantly expressed in the tumor tissues and plasma of patients with BC, and they modulate gene expression affecting the proliferation, metastasis, and chemoresistance of BC by specifically binding and regulating the expression of microRNAs (miRNAs). Therefore, circRNAs can be used as novel potential diagnostic and prognostic markers, and therapeutic targets for BC. This article summarizes the properties, functions, and regulatory mechanisms of circRNAs, particularly current research on their association with BC proliferation, metastasis, and chemoresistance.
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Affiliation(s)
- Diya Liu
- Department of Thyroid and Breast Diseases, Shanghai Tenth People’s Hospital, Shanghai 200070, China
| | - Lin Fang
- Department of Thyroid and Breast Diseases, Shanghai Tenth People’s Hospital, Shanghai 200070, China
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Functional Role of circRNAs in the Regulation of Fetal Development, Muscle Development, and Lactation in Livestock. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5383210. [PMID: 33688493 PMCID: PMC7914090 DOI: 10.1155/2021/5383210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 01/23/2021] [Accepted: 02/05/2021] [Indexed: 01/04/2023]
Abstract
circRNAs are a class of endogenous noncoding RNA molecules with closed loop structures. They are mainly responsible for regulating gene expression in eukaryotic cells. With the emergence of high-throughput RNA sequencing (RNA-Seq) and new types of bioinformatics tools, thousands of circRNAs have been discovered, making circRNA one of the research hotspots. Recent studies have shown that circRNAs play an important regulatory role in the growth, reproduction, and formation of livestock products. They can not only regulate mammalian fetal growth and development but also have important regulatory effects on livestock muscle development and lactation. In this review, we briefly introduce the putative biogenic pathways and regulatory functions of circRNA and highlight our understanding of circRNA and its latest advances in fetal development, muscle development, and lactation biogenesis as well as expression in livestock. This review will provide a theoretical basis for the research and development of related industries.
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6
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Wang M, Wu M, Xie T, Chen J. Circular RNAs Sparkle in the Diagnosis and Theranostics of Hepatocellular Carcinoma. Front Genet 2021; 11:628655. [PMID: 33679871 PMCID: PMC7930616 DOI: 10.3389/fgene.2020.628655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Exonic circular RNAs (circRNAs) are a novel subgroup of non-coding RNAs, which are generated by a back-splicing mechanism of the exons or introns. Unlike the linear RNA, circRNA forms a covalently closed loop, and it normally appears more abundant than the linear products of its host gene. Due to the relatively high specificity and stability of circular RNAs in tissues and body fluid, circular RNAs have attracted widely scientific interest for its potential application in cancer diagnosis and as a guide for preclinical therapy, especially for hard-to-treat cancers with high heterogeneity, such as hepatocellular carcinoma (HCC). Thus, we summarize the updated knowledge of circular RNAs, including the mechanism of the generation of endogenous circular RNAs and their regulatory, diagnostic, and therapeutic roles in HCC.
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Affiliation(s)
- Menglan Wang
- College of Pharmacy, School of Medicine, Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The Affiliated Hospital of Hangzhou Normal University, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Minjie Wu
- College of Pharmacy, School of Medicine, Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The Affiliated Hospital of Hangzhou Normal University, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Tian Xie
- College of Pharmacy, School of Medicine, Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The Affiliated Hospital of Hangzhou Normal University, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Jianxiang Chen
- College of Pharmacy, School of Medicine, Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The Affiliated Hospital of Hangzhou Normal University, Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
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7
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Ma N, Zhang W, Wan J. Research Progress on circRNA in Nervous System Diseases. Curr Alzheimer Res 2020; 17:687-697. [DOI: 10.2174/1567205017666201111114928] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 12/19/2022]
Abstract
Circular RNAs (circRNAs) are a kind of non-coding RNA molecule with highly stable circular
structures. CircRNAs are primarily composed of exons and/or introns. Recently, a lot of exciting
studies showed that circRNA played an essential role in the development of nervous system diseases.
Here, classification, characteristics, biogenesis, and the association of circRNA dysregulation with nervous
system diseases, such as Alzheimer’s disease, are summarized. The review not only contributes to a
better understanding of circRNAs, but also provides new research directions toward the diagnosis, treatment,
and prevention of nervous system diseases.
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Affiliation(s)
- Nana Ma
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China
| | - Wei Zhang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China
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8
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Revealing Epigenetic Factors of circRNA Expression by Machine Learning in Various Cellular Contexts. iScience 2020; 23:101842. [PMID: 33319172 PMCID: PMC7725743 DOI: 10.1016/j.isci.2020.101842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
Circular RNAs (circRNAs) have been identified as naturally occurring RNAs that are highly represented in the eukaryotic transcriptome. Although a large number of circRNAs have been reported, the underlying regulatory mechanism of circRNAs biogenesis remains largely unknown. Here, we integrated in-depth multi-omics data including epigenome, transcriptome, and non-coding RNA and identified candidate circRNAs in six cellular contexts. Next, circRNAs were divided into two classes (high versus low) with different expression levels. Machine learning models were constructed that predicted circRNA expression levels based on 11 different histone modifications and host gene expression. We found that the models achieve great accuracy in predicting high versus low expressed circRNAs. Furthermore, the expression levels of host genes of circRNAs, H3k36me3, H3k79me2, and H4k20me1 contributed greatly to the classification models in six cellular contexts. In summary, all these results suggest that epigenetic modifications, particularly histone modifications, can effectively predict expression levels of circRNAs. CircRNAs exhibit specific expression in various cellular contexts High and low expressed circRNAs exhibit different biological functions Histone modifications are significantly correlated with circRNAs expression Machine learning models were constructed for predicting circRNAs expression
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Zhang P, Li S, Chen M. Characterization and Function of Circular RNAs in Plants. Front Mol Biosci 2020; 7:91. [PMID: 32509801 PMCID: PMC7248317 DOI: 10.3389/fmolb.2020.00091] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
CircRNAs are covalently closed-loop single-stranded RNA molecules ubiquitously expressing in eukaryotes. As an important member of the endogenous ncRNA family, circRNAs are associated with diverse biological processes and can regulate transcription, modulate alternative splicing, and interact with miRNAs or proteins. Compared to abundant advances in animals, studies of circRNAs in plants are rapidly emerging. The databases and analysis tools for plant circRNAs are constantly being developed. Large numbers of circRNAs have been identified and characterized in plants and proved to play regulatory roles in plant growth, development, and stress responses. Here, we review the biogenesis, characteristics, bioinformatics resources, and biological functions of plant circRNAs, and summarize the distinct circularization features and differentially expression patterns comparison with animal-related results.
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Affiliation(s)
- Peijing Zhang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
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10
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Zhang X, Ma X, Ning L, Li Z, Zhao K, Li K, He J, Yin D. Genome-wide identification of circular RNAs in peanut (Arachis hypogaea L.). BMC Genomics 2019; 20:653. [PMID: 31416415 PMCID: PMC6694679 DOI: 10.1186/s12864-019-6020-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/09/2019] [Indexed: 01/16/2023] Open
Abstract
Background Circular RNAs (circRNAs), a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and developmental processes in eukaryotic cells. However, there have been no related studies on the number of circRNAs and their overall characteristics including circRNA abundance and expression profiles in peanut, which is one of the most important edible oil seed crops in the world. Results We performed a genome-wide identification of circular RNAs using ribosomal-depleted RNA-sequencing from the seeds of two peanut eighth-generation recombinant inbred lines (RIL8): ‘RIL 8106’ (a medium-pod variety) and ‘RIL 8107’ (a super-pod variety), at 15 and 35 days after flowering (DAF), respectively. A total of 347 circRNA candidates were detected by two computational pipelines: CIRCexplorer and CIRI, with at least two supporting junction reads. All these circRNAs were generated from exons of annotated genes, and widespread on the 20 peanut chromosomes. The expression profiles revealed that circRNAs were differentially expressed between two stages and between two lines. GO enrichment analysis of the host genes produced differentially-expressed circRNAs suggested that circRNAs are involved in seed development and regulation of seed size. Fifteen circRNAs were experimentally analyzed by qRT-PCR with divergent primers, and six circRNAs were resistant to digestion with RNase R exonuclease, and the back-splicing sites were further validated by Sanger DNA sequencing. Conclusions We present the first systematical investigation of the genomic characteristics and expression profiles of circRNAs in peanut. The results revealed that circRNAs are abundant and widespread in peanut, and the differentially-expressed circRNAs between two lines suggested that they might play regulatory roles in peanut seeds development. Electronic supplementary material The online version of this article (10.1186/s12864-019-6020-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xingguo Zhang
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Xingli Ma
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Longlong Ning
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Zhongfeng Li
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Kunkun Zhao
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Ke Li
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Jialin He
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Dongmei Yin
- College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China.
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11
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George AK, Master K, Majumder A, Homme RP, Laha A, Sandhu HS, Tyagi SC, Singh M. Circular RNAs constitute an inherent gene regulatory axis in the mammalian eye and brain. Can J Physiol Pharmacol 2019; 97:463-472. [DOI: 10.1139/cjpp-2018-0505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Circular RNAs (circRNAs) are being hailed as a newly rediscovered class of covalently closed transcripts that are produced via alternative, noncanonical pre-mRNA back-splicing events. These single-stranded RNA molecules have been identified in organisms ranging from the worm (Cortés-López et al. 2018. BMC Genomics, 19: 8; Ivanov et al. 2015. Cell Rep. 10: 170–177) to higher eukaryotes (Yang et al. 2017. Cell Res. 27: 626–641) to plants (Li et al. 2017. Biochem. Biophys. Res. Commun. 488: 382–386). At present, research on circRNAs is an active area because of their diverse roles in development, health, and diseases. Partly because their circularity makes them resistant to degradation, they hold great promise as unique biomarkers for ocular and central nervous system (CNS) disorders. We believe that further work on their applications could help in developing them as “first-in-class” diagnostics, therapeutics, and prognostic targets for numerous eye conditions. Interestingly, many circRNAs play key roles in transcriptional regulation by acting as miRNAs sponges, meaning that they serve as master regulators of RNA and protein expression. Since the retina is an extension of the brain and is part of the CNS, we highlight the current state of circRNA biogenesis, properties, and function and we review the crucial roles that they play in the eye and the brain. We also discuss their regulatory roles as miRNA sponges, regulation of their parental genes or linear mRNAs, translation into micropeptides or proteins, and responses to cellular stress. We posit that future advances will provide newer insights into the fields of RNA metabolism in general and diseases of the aging eye and brain in particular. Furthermore, in keeping pace with the rapidly evolving discipline of RNA“omics”-centered metabolism and to achieve uniformity among researchers, we recently introduced the term “cromics” (circular ribonucleic acids based omics) (Singh et al. 2018. Exp. Eye Res. 174: 80–92).
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Affiliation(s)
- Akash K. George
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Kruyanshi Master
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Avisek Majumder
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rubens Petit Homme
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Anwesha Laha
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Harpal S. Sandhu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Kentucky Lions Eye Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Suresh C. Tyagi
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
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12
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The roles of circular RNAs in human development and diseases. Biomed Pharmacother 2019; 111:198-208. [DOI: 10.1016/j.biopha.2018.12.052] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 12/20/2022] Open
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13
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Tian F, Wang Y, Xiao Z, Zhu X. [Circular RNA CircHIPK3 Promotes NCI-H1299 and NCI-H2170 Cell Proliferation through miR-379 and its Target IGF1]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2018; 20:459-467. [PMID: 28738961 PMCID: PMC5972943 DOI: 10.3779/j.issn.1009-3419.2017.07.04] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
背景与目的 已有的研究证明:环状RNA是一类在哺乳动物中普遍存在的具有稳定闭合环状结构的内源性RNA分子。环状RNA circHIPK3(circular RNA HIPK3, circHIPK3)在肝细胞癌(hepatocellular carcinoma, HCC)中表达水平较高,促进肝癌细胞生长。但是其在非小细胞肺癌(non-small cell lung cancer, NSCLC)中的作用及其调控机制尚无文献报道。本研究拟探讨环状RNA circHIPK3对NSCLC细胞系NCI-H1299和NCI-H2170细胞增殖的影响,并进一步研究其调控的分子机制。 方法 Real-time PCR法检测circHIPK3在NSCLC各细胞系中的表达水平。CCK-8实验和克隆形成实验检测过量表达和干扰circHIPK3对细胞增殖的影响。双荧光素酶报告基因实验分别检验miR-379与circHIPK3及miR-379与IGF1 mRNA的结合情况。Western blot和ELISA检测细胞内外的IGF1蛋白表达水平。 结果 环状RNA circHIPK3在6株NSCLC细胞株中均有表达,其中H1299表达最低,H2170表达最高,通过转染过表达的circHIPK3可显著促进NCI-H1299细胞增殖,干扰circHIPK3可显著抑制NCI-H2170细胞增殖。miR-379可与circHIPK3及IGF1 mRNA直接结合。过表达circHIPK3导致IGF1表达量上调,干扰circHIPK3能够下调IGF1表达水平,转入miR-379 mimics恢复了circHIPK3稳转细胞株IGF1表达水平的上调及细胞增殖表型。 结论 环状RNA circHIPK3在NSCLC细胞系NCI-H1299及NCI-H2170中可通过miR-379调控IGF1表达促进细胞增殖,环状RNA circHIPK3可能成为非小细胞肺癌治疗的新靶点。
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Affiliation(s)
- Fang Tian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361000, China;Dpartment of Respiratory Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Yun Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361000, China
| | - Zhe Xiao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361000, China
| | - Xuejun Zhu
- Dpartment of Respiratory Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
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Chen D, Zhang C, Lin J, Song X, Wang H. Screening differential circular RNA expression profiles reveal that hsa_circ_0128298 is a biomarker in the diagnosis and prognosis of hepatocellular carcinoma. Cancer Manag Res 2018; 10:1275-1283. [PMID: 29849467 PMCID: PMC5965387 DOI: 10.2147/cmar.s166740] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aim The aim of this study was to analyze the diagnostic and prognostic values of the circular RNA (circRNA) hsa_circ_0128298 in hepatocellular carcinoma (HCC). Patients and methods The global circRNA expression was measured using circRNA microarray using three pairs of cancer and noncancerous tissues from HCC patients. The microarray analysis revealed that two circRNAs were differentially expressed in the three pairs of cancerous and noncancerous tissues. The higher levels of two representative circRNAs, such as hsa_circ_0128298 and hsa_circ_0091582, were further confirmed by real-time polymerase chain reaction. In addition, the association between the expression level of hsa_circ_0128298 and the clinicopathological features of patients with HCC was further analyzed. The clinical diagnosis value was confirmed by receiver operating characteristic (ROC) curve analysis. Independent prognostic factors of patient outcome were identified using the Cox regression model. The survival data were analyzed by the Kaplan-Meier method, and the differences were evaluated using log-rank tests. Two-sided P-values <0.05 were considered statistically significant. Results The expression levels of hsa_circ_0128298 in HCC were significantly higher than those of paratumorous tissues (P<0.001). Additionally, hsa_circ_0128298 was a diagnostic factor, with the area under the ROC curve of 0.668 (95% CI =0.503-0.794, P<0.001). The sensitivity and specificity values were 0.716 and 0.815, respectively. The AFP and hsa_circ_0128298 expression levels were independent prognostic factors. The overall survival of patients with low hsa_circ_0128298 expression was significantly higher than that of patients with high hsa_circ_0128298 expression. Conclusion hsa_circ_0128298 may promote proliferation and metastasis and potentially represents a novel diagnostic and prognostic biomarker for HCC patients. However, studies with larger sample size are needed to confirm our conclusion.
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Affiliation(s)
- Dawei Chen
- Department of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University.,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan
| | - Chenyue Zhang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai
| | - Jiamao Lin
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Xinyu Song
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan.,Department of Internal Medicine-Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, People's Republic of China
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15
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Shao Y, Chen Y. Pathophysiology and Clinical Utility of Non-coding RNAs in Epilepsy. Front Mol Neurosci 2017; 10:249. [PMID: 28848386 PMCID: PMC5554344 DOI: 10.3389/fnmol.2017.00249] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022] Open
Abstract
Epilepsy is a common neurologic disorder. The underlying pathological processes include synaptic strength, inflammation, ion channels, and apoptosis. Acting as epigenetic factors, non-coding RNAs (ncRNAs) participate in the regulation of pathophysiologic processes of epilepsy and are dysregulated during epileptogenesis. Aberrant expression of ncRNAs are observed in epilepsy patients and animal models of epilepsy. Furthermore, ncRNAs might also be used as biomarkers for diagnosis and the prognosis of treatment response in epilepsy. In this review, we will summarize the role of ncRNAs in the pathophysiology of epilepsy and the putative utilization of ncRNAs as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Yiye Shao
- Department of Neurology, Jinshan Hospital, Fudan UniversityShanghai, China.,Department of Neurology, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Yinghui Chen
- Department of Neurology, Jinshan Hospital, Fudan UniversityShanghai, China.,Department of Neurology, Shanghai Medical College, Fudan UniversityShanghai, China
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